LAMMPS (10 Mar 2021)
  using 1 OpenMP thread(s) per MPI task
# sample surface deposition script for molecules

units		lj
atom_style      bond
boundary        p p f

lattice		fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region          box block 0 5 0 5 0 10
create_box      3 box bond/types 1 extra/bond/per/atom 1
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
  1 by 1 by 1 MPI processor grid

region		substrate block INF INF INF INF INF 3
create_atoms	1 region substrate
Created 350 atoms
  create_atoms CPU = 0.001 seconds

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0
pair_coeff	1 2 1.0 1.0 5.0
mass		* 1.0

bond_style	harmonic
bond_coeff      1 5.0 1.0

neigh_modify	delay 0

molecule        dimer molecule.dimer
Read molecule template dimer:
  1 molecules
  2 atoms with max type 3
  1 bonds with max type 1
  0 angles with max type 0
  0 dihedrals with max type 0
  0 impropers with max type 0
region          slab block 0 5 0 5 8 9

group		addatoms empty
0 atoms in group addatoms
region          mobile block 0 5 0 5 2 INF
group		mobile region mobile
150 atoms in group mobile

compute	add addatoms temp
compute_modify	add dynamic/dof yes extra/dof 0

fix		1 addatoms rigid/nve/small molecule mol dimer
  create bodies CPU = 0.000 seconds
  0 rigid bodies with 0 atoms
  1.0000000 = max distance from body owner to body atom
fix		2 mobile langevin 0.1 0.1 0.1 587283
fix		3 mobile nve

fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0                 mol dimer vz -1.0 -1.0 rigid 1
fix		5 addatoms wall/reflect zhi EDGE

thermo_style	custom step atoms temp epair etotal press
thermo          100
thermo_modify	temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)

#dump		1 all atom 50 dump.deposit.atom

#dump		2 all image 50 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	2 pad 5

#dump		3 all movie 50 tmp.mpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	3 pad 5

run             10000
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.3
  ghost atom cutoff = 5.3
  binsize = 2.65, bins = 3 3 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes
Step Atoms Temp E_pair TotEng Press 
       0      350            0   -6.9215833   -6.9215833   -1.0052629 
     100      352    1.0079368   -6.8875167   -6.8803581  -0.73353914 
     200      354    1.0081552   -6.8594643   -6.8452248  -0.70421276 
     300      356    1.0085803   -6.8171524   -6.7959042   -0.6917826 
     400      358    1.0099188   -6.7852701   -6.7570601  -0.70371699 
     500      360    1.0140221   -6.7493429   -6.7141338  -0.68415307 
     600      362     1.026148   -6.7105231   -6.6680032  -0.68314418 
     700      364    1.0683344   -6.6725162    -6.621154  -0.65747369 
     800      366    1.0958953   -6.6412275   -6.5813425  -0.68789615 
     900      368    1.1250034   -6.6101882    -6.541404  -0.66674346 
    1000      370    1.2326365   -6.5993719   -6.5160856  -0.69688655 
    1100      372    1.1397444   -6.5912865   -6.5070312   -0.6333041 
    1200      374    1.0514447   -6.5905753   -6.5062348  -0.71020272 
    1300      376    1.0033284   -6.5747792   -6.4880554  -0.65459641 
    1400      378   0.82996548   -6.5681806   -6.4913319  -0.60438595 
    1500      380   0.90239071   -6.5752982   -6.4862465  -0.66528503 
    1600      382   0.86403681   -6.5692212   -6.4787461  -0.65027922 
    1700      384   0.64748046   -6.5644242   -6.4927629  -0.63046709 
    1800      386   0.74288742   -6.5515741   -6.4649681  -0.67770665 
    1900      388   0.72584537   -6.5565195   -6.4676596  -0.66175025 
    2000      390   0.73351281   -6.5631154   -6.4690753  -0.64686647 
    2100      392   0.76490681   -6.5573734   -6.4549305  -0.68861526 
    2200      394   0.65926638   -6.5511574   -6.4591279  -0.71726284 
    2300      396   0.70267414   -6.5728555   -6.4708258  -0.64360436 
    2400      398   0.60523691   -6.5845973   -6.4933555  -0.63956839 
    2500      400    0.5103586   -6.5812006   -6.5014571  -0.68698448 
    2600      402   0.52401744   -6.6003358   -6.5156066  -0.68987222 
    2700      404   0.46421291   -6.5662747   -6.4887143  -0.72872856 
    2800      406   0.48254258   -6.5724266   -6.4892296  -0.75447872 
    2900      408   0.53073083   -6.5809842   -6.4866754  -0.67592283 
    3000      410   0.55314547   -6.5922077   -6.4910226  -0.74646953 
    3100      412   0.47150308   -6.5907273   -6.5020344  -0.64994935 
    3200      414   0.43047803   -6.5836315   -6.5004473  -0.79764713 
    3300      416   0.46289353   -6.5739439   -6.4821441  -0.76441674 
    3400      418   0.59724106   -6.5980575   -6.4766089  -0.73735626 
    3500      420   0.43571285   -6.5955972   -6.5048237  -0.64145941 
    3600      422   0.42461639   -6.6060271   -6.5154691  -0.70124484 
    3700      424   0.44323254   -6.6059723   -6.5092766  -0.74498147 
    3800      426    0.4037907    -6.592043   -6.5019958  -0.72171799 
    3900      428   0.41668443   -6.5975302   -6.5026079  -0.68327878 
    4000      430   0.44895183   -6.5958671   -6.4914597  -0.73939433 
    4100      432   0.39798052   -6.5952115   -6.5007833  -0.74871822 
    4200      434   0.45156734   -6.6237274   -6.5144772  -0.75111778 
    4300      436   0.48297356   -6.6395283   -6.5204465  -0.76105913 
    4400      438   0.43595234   -6.6347133   -6.5252276  -0.72858275 
    4500      440   0.44683726   -6.6385398   -6.5242916  -0.74280051 
    4600      442   0.47875512   -6.6419903   -6.5174274  -0.75579572 
    4700      444   0.43972605   -6.6406078   -6.5242388  -0.72196509 
    4800      446   0.43572615   -6.6495404   -6.5323047   -0.7135049 
    4900      448   0.38063437   -6.6432385   -6.5391588  -0.77087429 
    5000      450    0.4239223   -6.6617795   -6.5440233    -0.784531 
    5100      452   0.37201988   -6.6581813   -6.5532421  -0.74611403 
    5200      454   0.41765777   -6.6661321   -6.5465385  -0.75422239 
    5300      456   0.38015287   -6.6606624   -6.5502013  -0.78866702 
    5400      458   0.40549607   -6.6807118   -6.5611878  -0.78932883 
    5500      460   0.34444407   -6.6720564   -6.5690976  -0.77859171 
    5600      462   0.36572308   -6.6730078   -6.5621827  -0.85672419 
    5700      464   0.40055073   -6.6976989    -6.574685  -0.74251563 
    5800      466   0.36037213   -6.7022014   -6.5900685  -0.66239625 
    5900      468   0.32810921   -6.6952135    -6.591803  -0.83981757 
    6000      470   0.35110886   -6.6986862   -6.5866302  -0.82474047 
    6100      472   0.29965884   -6.6839503   -6.5871326   -0.7864913 
    6200      474   0.32402637   -6.6902745   -6.5843165  -0.74531083 
    6300      476   0.35042653   -6.6990084   -6.5830585  -0.74839967 
    6400      478   0.32695511   -6.6909459   -6.5815048  -0.76549489 
    6500      480   0.35209088   -6.6902987   -6.5711013  -0.71281516 
    6600      482     0.354106   -6.6890268    -6.567808  -0.81897158 
    6700      484    0.3504816    -6.681739   -6.5604463    -0.811609 
    6800      486   0.37396733   -6.7018369   -6.5710253  -0.80383296 
    6900      488   0.36435774   -6.7010114   -6.5722169  -0.72063651 
    7000      490   0.35631012   -6.7089806    -6.581727  -0.74152078 
    7100      492   0.37646659    -6.719154   -6.5833352  -0.77739001 
    7200      494   0.36546269   -6.7223269   -6.5891623   -0.8288767 
    7300      496   0.37688206   -6.7457243    -6.607053  -0.80062121 
    7400      498   0.30331409   -6.7284953   -6.6158184  -0.79894584 
    7500      500   0.30382936   -6.7333804   -6.6194444  -0.86924602 
    7600      502   0.30163143   -6.7294737   -6.6153104   -0.7689497 
    7700      504   0.30281215   -6.7233976   -6.6077402   -0.8557548 
    7800      506   0.33378009   -6.7244958   -6.5958651  -0.82584084 
    7900      508   0.31843128   -6.7250998   -6.6013002  -0.82424684 
    8000      510   0.35912946   -6.7399052   -6.5990701  -0.81879575 
    8100      512   0.31405017    -6.733487   -6.6092777  -0.72940457 
    8200      514      0.30475   -6.7271485   -6.6056043  -0.87958287 
    8300      516   0.30717434   -6.7277574   -6.6042329  -0.81700937 
    8400      518   0.33032462   -6.7382165   -6.6043011  -0.75436496 
    8500      520   0.32218568   -6.7351971   -6.6035347  -0.77661738 
    8600      522   0.30922651   -6.7275431   -6.6001797  -0.85334327 
    8700      524   0.30728021   -6.7237477   -6.5962029  -0.94977016 
    8800      526   0.31061903   -6.7181672   -6.5882505  -0.86132456 
    8900      528   0.33543344    -6.728929   -6.5875768  -0.87545919 
    9000      530   0.31887735   -6.7265066   -6.5911341  -0.76892061 
    9100      532   0.31888326   -6.7216274   -6.5852629  -0.83190298 
    9200      534   0.33310892   -6.7111349    -6.567661  -0.94282671 
    9300      536   0.34737171    -6.722515   -6.5718361  -0.95235602 
    9400      538   0.32752858   -6.7246204   -6.5815549  -0.86227131 
    9500      540   0.30665764   -6.7225391   -6.5876665  -0.87144326 
    9600      542   0.32747382   -6.7149245   -6.5699176  -0.86863105 
    9700      544   0.32463079   -6.7205757   -6.5758643  -0.85393932 
    9800      546   0.31517825   -6.7178961   -6.5764699  -0.81017759 
    9900      548   0.33649933   -6.7380644   -6.5860871  -0.80769312 
   10000      550   0.37394555   -6.7612874   -6.5913121  -0.82102213 
Loop time of 16.7275 on 1 procs for 10000 steps with 550 atoms

Performance: 258256.688 tau/day, 597.816 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 9.2508     | 9.2508     | 9.2508     |   0.0 | 55.30
Bond    | 0.021603   | 0.021603   | 0.021603   |   0.0 |  0.13
Neigh   | 4.5325     | 4.5325     | 4.5325     |   0.0 | 27.10
Comm    | 0.62777    | 0.62777    | 0.62777    |   0.0 |  3.75
Output  | 0.006916   | 0.006916   | 0.006916   |   0.0 |  0.04
Modify  | 2.218      | 2.218      | 2.218      |   0.0 | 13.26
Other   |            | 0.07002    |            |       |  0.42

Nlocal:        550.000 ave         550 max         550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        2344.00 ave        2344 max        2344 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        36607.0 ave       36607 max       36607 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 36607
Ave neighs/atom = 66.558182
Ave special neighs/atom = 0.36363636
Neighbor list builds = 847
Dangerous builds = 0
Total wall time: 0:00:16
